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Cadmium in PDB 4bpk: Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5

Protein crystallography data

The structure of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5, PDB code: 4bpk was solved by B.J.Smith, E.F.Lee, J.W.Checco, S.H.Gellman, W.D.Fairlie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.066 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.175, 72.133, 80.579, 90.00, 90.00, 90.00
R / Rfree (%) 21.92 / 25.22

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Cadmium atom in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 (pdb code 4bpk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 19 binding sites of Cadmium where determined in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5, PDB code: 4bpk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 19 in 4bpk

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Cadmium binding site 1 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1196

b:44.4
occ:0.68
CD A:CD1196 0.0 44.4 0.7
CD A:CD1196 2.0 45.3 0.3
OE2 A:GLU129 2.4 44.7 1.0
O A:HOH2059 2.5 47.2 1.0
CD A:GLU129 3.4 43.6 1.0
OE1 A:GLU129 3.9 40.3 1.0
CB C:ALA7 3.9 43.7 1.0
NH2 C:ARG10 4.0 43.7 1.0
CG A:GLU129 4.7 36.8 1.0

Cadmium binding site 2 out of 19 in 4bpk

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Cadmium binding site 2 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1196

b:45.3
occ:0.32
CD A:CD1196 0.0 45.3 0.3
CD A:CD1196 2.0 44.4 0.7
OE2 A:GLU129 2.4 44.7 1.0
OE1 A:GLU129 2.5 40.3 1.0
CD A:GLU129 2.8 43.6 1.0
O A:HOH2059 3.7 47.2 1.0
CD A:ARG132 3.8 57.7 0.5
NH2 C:ARG10 4.3 43.7 1.0
CG A:GLU129 4.3 36.8 1.0
NE A:ARG132 4.3 60.0 0.5
NE A:ARG132 4.4 60.7 0.5
CG A:ARG132 4.6 59.2 0.5
CG A:ARG132 4.8 57.7 0.5
NH2 A:ARG132 4.8 49.9 0.5
CZ A:ARG132 4.9 56.1 0.5
CD A:ARG132 5.0 61.2 0.5

Cadmium binding site 3 out of 19 in 4bpk

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Cadmium binding site 3 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1197

b:56.4
occ:1.00
O A:HOH2042 2.3 53.8 1.0
OE2 A:GLU92 2.4 44.0 1.0
O A:HOH2043 2.4 55.2 1.0
O A:HOH2023 2.5 43.1 1.0
CD A:GLU92 3.3 46.9 1.0
OE1 A:GLU92 3.6 49.9 1.0
O A:SER18 3.8 40.1 0.7
O A:SER18 3.9 42.8 0.3
NE2 A:GLN88 4.2 36.8 1.0
O A:HOH2008 4.3 61.8 1.0
CG A:GLN88 4.3 35.7 1.0
O A:HOH2035 4.4 38.6 0.4
CG A:GLU92 4.6 41.4 1.0
CD A:GLN88 4.7 38.1 1.0
C A:SER18 4.8 40.2 0.3
C A:SER18 4.8 40.4 0.7
CB A:SER18 5.0 37.0 0.7

Cadmium binding site 4 out of 19 in 4bpk

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Cadmium binding site 4 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1198

b:69.0
occ:1.00
CD2 A:HIS113 2.8 56.7 0.5
NE2 A:HIS113 2.9 56.2 0.5
ND1 A:HIS113 3.2 62.3 0.5
CE1 A:HIS113 3.7 63.0 0.5
CG A:HIS113 4.0 57.9 0.5
CE1 A:HIS113 4.1 56.2 0.5
CG A:HIS113 4.3 62.6 0.5
O A:HOH2066 4.4 57.4 1.0
NZ A:LYS157 4.6 64.7 1.0
ND1 A:HIS113 4.7 52.2 0.5
CB A:HIS113 4.8 60.0 0.5
NE2 A:HIS113 4.9 64.4 0.5

Cadmium binding site 5 out of 19 in 4bpk

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Cadmium binding site 5 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1199

b:46.9
occ:1.00
OE1 A:GLU153 2.3 49.7 1.0
O A:HOH2051 2.4 56.5 1.0
O A:HOH2065 2.4 46.1 1.0
O A:HOH2064 2.4 70.3 1.0
OE2 A:GLU153 2.4 51.0 1.0
O A:HOH2066 2.6 57.4 1.0
CD A:GLU153 2.7 41.0 1.0
CE A:LYS157 4.0 55.6 1.0
CG A:GLU153 4.2 38.0 1.0
O A:HOH2050 4.3 59.3 1.0
O A:LEU112 4.5 58.3 1.0
O A:HOH2063 4.6 42.4 1.0
NZ A:LYS157 4.6 64.7 1.0
OD2 A:ASP156 4.8 52.0 1.0
O A:THR109 4.9 44.1 1.0
CB A:GLU153 5.0 35.0 1.0
O A:SER110 5.0 51.7 1.0

Cadmium binding site 6 out of 19 in 4bpk

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Cadmium binding site 6 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1200

b:62.3
occ:0.45
CD A:CD1200 0.0 62.3 0.5
CD A:CD1200 1.8 64.1 0.6
CE1 A:HIS177 2.6 56.9 0.6
NE2 A:HIS177 3.3 56.3 0.6
CE1 A:HIS177 3.3 56.5 0.4
ND1 A:HIS177 3.7 60.5 0.6
ND1 A:HIS177 4.0 57.4 0.4
NE2 A:HIS177 4.1 55.9 0.4
OD2 A:ASP176 4.3 69.2 0.4
CD2 A:HIS177 4.5 56.0 0.6
CB A:ASP176 4.5 63.8 0.4
CB A:ASP176 4.7 65.2 0.6
CG A:HIS177 4.7 56.5 0.6
OD2 A:ASP176 4.8 70.8 0.6
CG A:ASP176 4.9 67.9 0.4

Cadmium binding site 7 out of 19 in 4bpk

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Cadmium binding site 7 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1200

b:64.1
occ:0.55
CD A:CD1200 0.0 64.1 0.6
CD A:CD1200 1.8 62.3 0.5
CE1 A:HIS177 2.9 56.9 0.6
NE2 A:HIS177 3.1 56.3 0.6
CE1 A:HIS177 3.2 56.5 0.4
NE2 A:HIS177 3.5 55.9 0.4
ND1 A:HIS177 3.8 60.5 0.6
ND1 A:HIS177 4.0 57.4 0.4
CD2 A:HIS177 4.1 56.0 0.6
CD2 A:HIS177 4.4 53.9 0.4
CG A:HIS177 4.5 56.5 0.6
CG A:HIS177 4.7 53.4 0.4

Cadmium binding site 8 out of 19 in 4bpk

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Cadmium binding site 8 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1201

b:53.8
occ:1.00
O A:HOH2069 2.2 51.0 1.0
O A:HOH2068 2.2 52.7 1.0
OE2 A:GLU179 2.4 61.9 1.0
OE1 A:GLU179 2.7 55.5 1.0
CD A:GLU179 2.9 58.5 1.0
N B:SER2 4.1 68.3 1.0
CG A:GLU179 4.4 54.4 1.0
ND2 B:ASN5 4.6 54.6 1.0
OD1 A:ASN175 4.6 60.7 1.0
CB B:SER2 4.7 84.5 1.0
CA B:SER2 5.0 76.0 1.0

Cadmium binding site 9 out of 19 in 4bpk

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Cadmium binding site 9 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1196

b:47.5
occ:1.00
OD1 B:ASP189 2.4 67.1 1.0
OD2 B:ASP189 2.4 57.7 1.0
O B:GLY186 2.6 40.8 1.0
CG B:ASP189 2.7 57.8 1.0
O B:HOH2069 2.7 58.9 1.0
C B:GLY186 3.3 40.9 1.0
CA B:GLY186 4.0 44.0 1.0
N B:GLY187 4.1 37.4 1.0
OG1 B:THR190 4.2 50.0 1.0
CB B:ASP189 4.2 53.0 1.0
CA B:GLY187 4.2 32.7 1.0
N B:THR190 4.8 38.5 1.0
C B:GLY187 4.8 36.7 1.0

Cadmium binding site 10 out of 19 in 4bpk

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Cadmium binding site 10 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1197

b:47.7
occ:1.00
O B:HOH2073 2.3 77.7 1.0
O B:HOH2058 2.3 66.2 1.0
O B:HOH2074 2.4 56.2 1.0
OD2 B:ASP176 2.5 46.0 1.0
OD1 B:ASP176 2.6 46.1 1.0
CG B:ASP176 2.9 43.7 1.0
O B:HOH2061 4.0 59.2 1.0
CG2 B:THR172 4.0 30.1 1.0
CB B:ASP176 4.5 37.4 1.0
O B:HOH2060 4.9 34.8 1.0
O B:THR172 5.0 26.4 1.0

Reference:

B.J.Smith, E.F.Lee, J.W.Checco, M.Evangelista, S.H.Gellman, W.D.Fairlie. Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity For Bcl-2 Family Prosurvival Proteins. Chembiochem V. 14 1564 2013.
ISSN: ISSN 1439-4227
PubMed: 23929624
DOI: 10.1002/CBIC.201300351
Page generated: Sat Dec 12 08:24:07 2020

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